[gmx-users] Difference in properties when method of adding urea molecules is changed in a simulation box

[André Farias de Moura]

Hi Apramita,

you have not told us how many urea molecules you have added to you system,
neither have you told how large your peptide of interest is, but usually
people studying denaturation of peptides use very concentrated urea
solutions (typically 8 M or so), which are highly viscous.

If this is your case, 10 ns is certainly too short for equilibration and 20
ns is also way too short for structural sampling, I would increase both by
maybe 5-10 fold longer if proper relaxation and sampling are expected (how
long is long enough can be monitored by the time evolution of the
properties of interest - only when plateaus are obtained you can begin the
production run)

Andre


On Sun, Jun 4, 2017 at 12:39 PM, Apramita Chand <apramita.chand at gmail.com>
wrote:

> Dear All,
>
> I have tested with two ways of solvating a peptide with urea-water mixture
> Method 1: Pre-equilibrating a urea-water box and solvating the peptide with
> -cs option with this box
>
> Method 2: Adding urea molecules to peptide box using -ci option and then
> solvating the resulting box with water molecules
>
> In both the methods, same number of urea and water molecules were added .
> 10ns equilibration followed by 20ns simulation steps were carried out.
> On analysing the properties, average number of hydrogen bonds between
> peptide-water in method 1 was 16.221 while it changed to 14.340 in Method
> 2. Similarly, number of H-bonds between peptide-urea changed from 5.687 to
> 4.031 on switching from Method 1 to Method 2.
>
> On checking radial distribution functions, interaction between
> water-peptide sites were somewhat similar for both Methods but significant
> changes were found for peptide-urea site-site correlations. Method-1 showed
> higher peptide-urea interaction.
>
> What could be the reason for these discrepancies? Are both methods correct?
> I want to go on with Method-2 for further simulations because it is
> relatively simpler but Method-1 shows higher hydrogen bonding between
> sites.
>
> Please suggest.
>
> yours sincerely,
> Apramita
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
_____________

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090